Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  S. CEREVISIAE OROTATE PHOSPHORIBOSYLTRANSFERASE COMPLEXED WITH OROTIC ACID AND PRPP
 
Authors :  L. Gonzalez-Segura, T. D. Hurley, R. W. Mcclard
Date :  04 May 07  (Deposition) - 15 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha Beta, Oprtase-Oa-Prpp Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Gonzalez-Segura, J. F. Witte, R. W. Mcclard, T. D. Hurley
Ternary Complex Formation And Induced Asymmetry In Orotate Phosphoribosyltransferase.
Biochemistry V. 46 14075 2007
PubMed-ID: 18020427  |  Reference-DOI: 10.1021/BI701023Z

(-) Compounds

Molecule 1 - OROTATE PHOSPHORIBOSYLTRANSFERASE 1
    Chains: A, B
    EC Number: 2.4.2.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PREJ2
    Expression System Strain: CS101-4UI
    Expression System Taxid: 562
    Expression System Vector Type: PTRC99A
    Gene: URA5, PYR5
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: OPRT 1, OPRTASE 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2ORO2Ligand/IonOROTIC ACID
3PRP2Ligand/IonALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRP A:700 , HOH A:721 , HOH A:834BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWAREPRP B:800 , HOH B:833 , HOH B:877BINDING SITE FOR RESIDUE MG B 402
3AC3SOFTWARELEU A:28 , LYS A:29 , PHE A:37 , PHE A:38 , ASP A:132 , THR A:135 , ARG A:163 , PRP A:700 , HOH A:702 , HOH A:703 , HOH A:705 , HOH A:728BINDING SITE FOR RESIDUE ORO A 500
4AC4SOFTWAREHOH A:713 , LEU B:28 , LYS B:29 , PHE B:37 , PHE B:38 , ASP B:132 , THR B:135 , ARG B:163 , PRP B:800 , HOH B:801 , HOH B:802 , HOH B:803BINDING SITE FOR RESIDUE ORO B 600
5AC5SOFTWARELYS A:29 , TYR A:75 , LYS A:76 , ASP A:131 , ASP A:132 , VAL A:133 , THR A:135 , ALA A:136 , GLY A:137 , THR A:138 , ALA A:139 , MG A:401 , ORO A:500 , HOH A:701 , HOH A:702 , HOH A:703 , HOH A:705 , HOH A:712 , HOH A:721 , HOH A:789 , HOH A:799 , HOH A:801 , ARG B:105 , LYS B:109 , HIS B:111BINDING SITE FOR RESIDUE PRP A 700
6AC6SOFTWAREARG A:105 , LYS A:109 , HIS A:111 , HOH A:704 , HOH A:713 , LYS B:29 , TYR B:75 , LYS B:76 , ASP B:131 , ASP B:132 , VAL B:133 , THR B:135 , ALA B:136 , GLY B:137 , THR B:138 , ALA B:139 , MG B:402 , ORO B:600 , HOH B:802 , HOH B:803 , HOH B:814 , HOH B:833 , HOH B:899 , HOH B:908 , HOH B:914BINDING SITE FOR RESIDUE PRP B 800

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PS1)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ala A:74 -Tyr A:75
2Thr A:207 -Ala A:208
3Ala B:74 -Tyr B:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PS1)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUR_PYR_PR_TRANSFERPS00103 Purine/pyrimidine phosphoribosyl transferases signature.PYRE_YEAST128-140
 		  2A:127-139
B:127-139

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YML106W1YML106W.1XIII:56773-57453681PYRE_YEAST1-2262262A:2-225
B:2-225		224
224

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:224
 aligned with PYRE_YEAST | P13298 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:224
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222    
           PYRE_YEAST     3 IMLEDYQKNFLELAIECQALRFGSFKLKSGRESPYFFNLGLFNTGKLLSNLATAYAIAIIQSDLKFDVIFGPAYKGIPLAAIVCVKLAEIGGSKFQNIQYAFNRKEAKDHGEGGIIVGSALENKRILIIDDVMTAGTAINEAFEIISNAKGQVVGSIIALDRQEVVSTDDKEGLSATQTVSKKYGIPVLSIVSLIHIITYLEGRITAEEKSKIEQYLQTYGASA 226
               SCOP domains d2ps1a_ A: automated matches                                                                                                                                                                                                     SCOP domains
               CATH domains 2ps1A00 A:2-225  [code=3.40.50.2020, no name defined]                                                                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh..eeeeeee.....eeeeee.hhhh.hhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhhhh.......eeeeeeeeee.....eeeee......eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeee.............hhhhhhhhhhh..eeeeeehhhhhhhhhhhh..hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR-------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:2-225 UniProt: 1-226 [INCOMPLETE]                                                                                                                                                                               Transcript 1
                 2ps1 A   2 IMLEDYQKNFLELAIECQALRFGSFKLKSGRESPYFFNLGLFNTGKLLSNLATAYAIAIIQSDLKFDVIFGPAYKGIPLAAIVCVKLAEIGGSKFQNIQYAFNRKEAKDHGEGGIIVGSALENKRILIIDDVMTAGTAINEAFEIISNAKGQVVGSIIALDRQEVVSTDDKEGLSATQTVSKKYGIPVLSIVSLIHIITYLEGRITAEEKSKIEQYLQTYGASA 225
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221    


Chain B from PDB  Type:PROTEIN  Length:224
 aligned with PYRE_YEAST | P13298 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:224
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222    
           PYRE_YEAST     3 IMLEDYQKNFLELAIECQALRFGSFKLKSGRESPYFFNLGLFNTGKLLSNLATAYAIAIIQSDLKFDVIFGPAYKGIPLAAIVCVKLAEIGGSKFQNIQYAFNRKEAKDHGEGGIIVGSALENKRILIIDDVMTAGTAINEAFEIISNAKGQVVGSIIALDRQEVVSTDDKEGLSATQTVSKKYGIPVLSIVSLIHIITYLEGRITAEEKSKIEQYLQTYGASA 226
               SCOP domains d2ps1b_ B: automated matches                                                                                                                                                                                                     SCOP domains
               CATH domains 2ps1B00 B:2-225  [code=3.40.50.2020, no name defined]                                                                                                                                                                            CATH domains
           Pfam domains (1) --------------------------------------Pribosyltran-2ps1B01 B:40-161                                                                                             ---------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------Pribosyltran-2ps1B02 B:40-161                                                                                             ---------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhh..eeeeeee.....eeeeee.hhhh.hhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee.....eeeee......eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeee.............hhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR-------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:2-225 UniProt: 1-226 [INCOMPLETE]                                                                                                                                                                               Transcript 1
                 2ps1 B   2 IMLEDYQKNFLELAIECQALRFGSFKLKSGRESPYFFNLGLFNTGKLLSNLATAYAIAIIQSDLKFDVIFGPAYKGIPLAAIVCVKLAEIGGSKFQNIQYAFNRKEAKDHGEGGIIVGSALENKRILIIDDVMTAGTAINEAFEIISNAKGQVVGSIIALDRQEVVSTDDKEGLSATQTVSKKYGIPVLSIVSLIHIITYLEGRITAEEKSKIEQYLQTYGASA 225
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PRTase-like (59)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PYRE_YEAST | P13298)
molecular function
    GO:0004588    orotate phosphoribosyltransferase activity    Catalysis of the reaction: orotidine 5'-phosphate + diphosphate = orotate + 5-phospho-alpha-D-ribose 1-diphosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0044205    'de novo' UMP biosynthetic process    The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD(+) or oxygen.
    GO:0006207    'de novo' pyrimidine nucleobase biosynthetic process    The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
    GO:0009116    nucleoside metabolic process    The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
    GO:0006221    pyrimidine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0046132    pyrimidine ribonucleoside biosynthetic process    The chemical reactions and pathways resulting in the formation of any ribonucleoside, a nucleoside in which a pyrimidine base is linked to a ribose (beta-D-ribofuranose) molecule.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ORO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PRP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:74 - Tyr A:75   [ RasMol ]  
    Ala B:74 - Tyr B:75   [ RasMol ]  
    Thr A:207 - Ala A:208   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2ps1
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PYRE_YEAST | P13298
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.4.2.10
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PYRE_YEAST | P13298
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PYRE_YEAST | P13298: 2pry 2prz 4wml 4wn3

(-) Related Entries Specified in the PDB File

2pry THE SAME PROTEIN IN THE APO FORM
2prz THE SAME PROTEIN COMPLEXED WITH OMP